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Article ; Online: Redesigning green revolution trait with increased grain yield and nitrogen utilization efficiency by reducing brassinosteroid signaling in semidwarf wheat.

Guo, Hongqing / Yin, Yanhai

2023 Volume 66, Issue 10, Page(s) 2448–2450

MeSH term(s)	Triticum/genetics ; Brassinosteroids ; Edible Grain/genetics ; Agriculture ; Nitrogen
Chemical Substances	Brassinosteroids ; Nitrogen (N762921K75)
Language	English
Publishing date	2023-06-29
Publishing country	China
Document type	Journal Article
ZDB-ID	2546732-3
ISSN	1869-1889 ; 1674-7305
ISSN (online)	1869-1889
ISSN	1674-7305
DOI	10.1007/s11427-023-2401-3
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Information-incorporated gene network construction with FDR control.

Wang, Hao / Qiu, Yumou / Guo, Hongqing / Yin, Yanhai / Liu, Peng

Bioinformatics (Oxford, England)

2024 Volume 40, Issue 3

Abstract: Motivation: Large-scale gene expression studies allow gene network construction to uncover associations among genes. To study direct associations among genes, partial correlation-based networks are preferred over marginal correlations. However, FDR ... ...

Abstract	Motivation: Large-scale gene expression studies allow gene network construction to uncover associations among genes. To study direct associations among genes, partial correlation-based networks are preferred over marginal correlations. However, FDR control for partial correlation-based network construction is not well-studied. In addition, currently available partial correlation-based methods cannot take existing biological knowledge to help network construction while controlling FDR. Results: In this paper, we propose a method called Partial Correlation Graph with Information Incorporation (PCGII). PCGII estimates partial correlations between each pair of genes by regularized node-wise regression that can incorporate prior knowledge while controlling the effects of all other genes. It handles high-dimensional data where the number of genes can be much larger than the sample size and controls FDR at the same time. We compare PCGII with several existing approaches through extensive simulation studies and demonstrate that PCGII has better FDR control and higher power. We apply PCGII to a plant gene expression dataset where it recovers confirmed regulatory relationships and a hub node, as well as several direct associations that shed light on potential functional relationships in the system. We also introduce a method to supplement observed data with a pseudogene to apply PCGII when no prior information is available, which also allows checking FDR control and power for real data analysis. Availability and implementation: R package is freely available for download at https://cran.r-project.org/package=PCGII.
MeSH term(s)	Gene Regulatory Networks ; Algorithms ; Computer Simulation ; Genes, Plant ; Sample Size
Language	English
Publishing date	2024-03-02
Publishing country	England
Document type	Journal Article
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btae125
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Article: Updates on BES1/BZR1 Regulatory Networks Coordinating Plant Growth and Stress Responses.

Kono, Alfredo / Yin, Yanhai

Frontiers in plant science

2020 Volume 11, Page(s) 617162

Abstract: Brassinosteroids (BRs) play pivotal roles in the regulation of many dimensions of a plant's life. Hence, through extensive efforts from many research groups, BR signaling has emerged as one of the best-characterized plant signaling pathways. The key ... ...

Abstract	Brassinosteroids (BRs) play pivotal roles in the regulation of many dimensions of a plant's life. Hence, through extensive efforts from many research groups, BR signaling has emerged as one of the best-characterized plant signaling pathways. The key molecular players of BR signaling from the cell surface to the nucleus important for the regulation of plant growth and development are well-established. Recent data show that BRs also modulate plant responses to environmental stresses such as drought and pathogen infection. In this mini review, we present the recent progress in BR signaling specifically in the post-translational SUMO modification of BR's master regulators, BES1/BZR1. We also discuss recent findings on the crosstalk between BR, UV light, and jasmonic acid signaling pathways to balance growth during light stress and pathogen infections. Finally, we describe the current update on the molecular link between BR signaling and intracellular auxin transport that essential for plant development.
Language	English
Publishing date	2020-12-03
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2711035-7
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2020.617162
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Article ; Online: Interactions between autophagy and phytohormone signaling pathways in plants.

Liao, Ching-Yi / Wang, Ping / Yin, Yanhai / Bassham, Diane C

FEBS letters

2022 Volume 596, Issue 17, Page(s) 2198–2214

Abstract: Autophagy is a conserved recycling process with important functions in plant growth, development, and stress responses. Phytohormones also play key roles in the regulation of some of the same processes. Increasing evidence indicates that a close ... ...

Abstract	Autophagy is a conserved recycling process with important functions in plant growth, development, and stress responses. Phytohormones also play key roles in the regulation of some of the same processes. Increasing evidence indicates that a close relationship exists between autophagy and phytohormone signaling pathways, and the mechanisms of interaction between these pathways have begun to be revealed. Here, we review recent advances in our understanding of how autophagy regulates hormone signaling and, conversely, how hormones regulate the activity of autophagy, both in plant growth and development and in environmental stress responses. We highlight in particular recent mechanistic insights into the coordination between autophagy and signaling events controlled by the stress hormone abscisic acid and by the growth hormones brassinosteroid and cytokinin and briefly discuss potential connections between autophagy and other phytohormones.
MeSH term(s)	Autophagy ; Cytokinins/metabolism ; Hormones/metabolism ; Plant Growth Regulators/metabolism ; Plants/genetics ; Plants/metabolism ; Signal Transduction/physiology
Chemical Substances	Cytokinins ; Hormones ; Plant Growth Regulators
Language	English
Publishing date	2022-04-28
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1002/1873-3468.14355
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Article: Comparison of effectiveness and postoperative complications of different surgical methods in the treatment of benign prostatic hyperplasia: a systematic review and meta-analysis based on randomized controlled trials.

Fu, Yujia / Wen, Xiaomiao / Yin, Yanhai / Wang, Chaoqun / Mai, Jiren

Translational andrology and urology

2022 Volume 11, Issue 6, Page(s) 842–858

Abstract: Background: More and more new surgical procedures for the treatment of benign prostate hyperplasia (BPH) are proposed creatively. However, the existing clinical evidence shows that the effectiveness and safety of various procedures exist inconsistent.!## ...

Abstract	Background: More and more new surgical procedures for the treatment of benign prostate hyperplasia (BPH) are proposed creatively. However, the existing clinical evidence shows that the effectiveness and safety of various procedures exist inconsistent. Methods: The randomized controlled trials comparing the international prostate score, length of hospital stay, maximum urinary flow rate, operation time, and complication rates of prostatic artery embolization (PAE), Greenlight-XPS Laser prostate vaporization procedure (GLL PVP), diode laser enucleation of prostate (DILEP) and plasmakinetic resection of the prostate (PKRP), transurethral resection of the prostate (TURP) in patients with BPH were screened out in databases. The primary outcome was pooled using a restricted maximum likelihood-based random-effect model and inverse variance-based fixed-effect model. Cochrane Q statistics and I2 statistics were computed to quantify between-study heterogeneity. The risk of bias of each included study was assessed using the revised Cochrane risk of bias tool. Results: This meta-analysis ultimately included 14 original research papers, with 1,940 participants enrolled. Eight studies were considered to be at moderate risk of bias, while the others were at mild risk of bias. Although the improvement in functional outcome of the DILEP procedure was equivalent to that of the PKRP procedure, the DILEP procedure group had fewer hospital stays than the PKRP group (P=0.01). In addition, even though the performance of the GLL PVP procedure in the improvement of functional outcome was inferior to the counterpart of TURP (P=0.64), it had a much fewer hospital stays (P=0.01). Moreover, there is still insufficient evidence for the improvement of subjective functional indicators of postoperative patients with PAE compared with TURP [international prostate symptom score (IPSS): P=0.73; IPSS QoL: P=0.91], but achieved less satisfactory objective functional outcomes (Qmax: P=0.06; PVR: P=0.00). Discussion: New surgical procedures such as GLL PVP, PAE, and DILEP were safer than traditional TURP procedures. However, it is not superior to traditional surgery in the improvement of clinical symptoms. In clinical practice, the pros and cons of the new operation and the traditional operation should be carefully weighed, and the operation that is most suitable for the patient's condition should be selected.
Language	English
Publishing date	2022-07-04
Publishing country	China
Document type	Journal Article
ZDB-ID	2851630-8
ISSN	2223-4691 ; 2223-4691 ; 2223-4683
ISSN (online)	2223-4691
ISSN	2223-4691 ; 2223-4683
DOI	10.21037/tau-22-377
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Article ; Online: Measuring Protein Half-life in

Guo, Hongqing / Yin, Yanhai

Bio-protocol

2019 Volume 9, Issue 15, Page(s) e3318

Abstract: Post-translational modifications play important roles in controlling protein function and can lead to altered protein stability. Protein stability can be determined after treatment with the protein synthesis inhibitor Cycloheximide. Cycloheximide is a ... ...

Abstract	Post-translational modifications play important roles in controlling protein function and can lead to altered protein stability. Protein stability can be determined after treatment with the protein synthesis inhibitor Cycloheximide. Cycloheximide is a translational inhibitor that inhibits protein synthesis via cytoplasmic ribosomes. Here we describe how to measure the stability of MYC2 in the context of regulation by FERONIA receptor kinase. First, we describe how to measure MYC2 stability in wild-type and
Language	English
Publishing date	2019-08-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	2833269-6
ISSN	2331-8325 ; 2331-8325
ISSN (online)	2331-8325
ISSN	2331-8325
DOI	10.21769/BioProtoc.3318
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Article ; Online: CYP4B1 polymorphisms and the risk of breast cancer in Chinese women: a case-control study.

Yin, Yanhai / Tong, Liangqian / Wan, Zhenling / Sui, Yanfang / Li, Fen / Huang, Qian / Zhao, Xinhan

BMC cancer

2023 Volume 23, Issue 1, Page(s) 1177

Abstract: Background: Breast cancer (BC) is one of the malignant diseases threatening the life and health of women worldwide. The CYP4B1 gene was abnormally expressed in BC and was associated with the prognosis of BC patients. This study aimed to explore the ... ...

Abstract	Background: Breast cancer (BC) is one of the malignant diseases threatening the life and health of women worldwide. The CYP4B1 gene was abnormally expressed in BC and was associated with the prognosis of BC patients. This study aimed to explore the relationship between CYP4B1 single nucleotide polymorphisms (SNPs) and BC risk in Chinese women. Methods: A case-control study of 1,143 women (571 patients and 572 healthy individuals) was conducted. Rs2297813 G/T, rs12142787 G/A, and rs3766197 C/T in CYP4B1 were selected and genotyped by MassARRAY system. The relationships between these SNPs and the risk of BC were assessed by logistic regression analysis. In addition, multi-factor dimensionality reduction (MDR) was used to analyze SNP-SNP interactions. Results: CYP4B1 rs2297813 had a risk-increasing effect on BC in women with body mass index (BMI) ≤ 24 kg/m Conclusion: CYP4B1 SNPs were associated with BC risk in Chinese women, especially in patients with BMI ≤ 24 kg/m
MeSH term(s)	Humans ; Female ; Breast Neoplasms/epidemiology ; Breast Neoplasms/genetics ; Breast Neoplasms/pathology ; Genetic Predisposition to Disease ; Case-Control Studies ; East Asian People ; Polymorphism, Single Nucleotide
Chemical Substances	cytochrome P-450 CYP4B1 (EC 1.14.14.1)
Language	English
Publishing date	2023-12-01
Publishing country	England
Document type	Journal Article
ZDB-ID	2041352-X
ISSN	1471-2407 ; 1471-2407
ISSN (online)	1471-2407
ISSN	1471-2407
DOI	10.1186/s12885-023-11477-y
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Article: A novel method of generating RNAi libraries for high‐throughput gene function analysis of creeping bentgrass

Hao, Jingjie / Ma, Conglie / Yin, Yanhai / Fei, Shui‐zhang

International Turfgrass Society research journal. 2022 June, v. 14, no. 1

2022

Abstract: RNA interference (RNAi) is a powerful tool for gene function analysis, particularly for outcrossing polyploid species where simultaneous mutations of multiple alleles of a gene with similar but nonidentical sequences may not be readily achieved with the ... ...

Abstract	RNA interference (RNAi) is a powerful tool for gene function analysis, particularly for outcrossing polyploid species where simultaneous mutations of multiple alleles of a gene with similar but nonidentical sequences may not be readily achieved with the novel clustered regularly interspaced short palindromic repeats/Cas9 gene editing tools. The most effective RNAi strategy in plants is to use long hairpin RNAi (lhRNAi) constructs containing inverted repeats (IRs) of target genes. Previously, we used a Phi29‐Amplified RNAi Construct method to create a single lhRNAi construct that was shown to be highly effective in gene silencing in the model grass Brachypodium distachyon (L.) P.Beauv. Here, we describe a method of creating a library of lhRNAi constructs ready for high‐throughput gene function analysis in creeping bentgrass (Agrostis stolonifera L.), an important turfgrass species. A cDNA population in which salt‐responsive genes were enriched by suppression subtractive hybridization was used as the source of IRs. Sequencing of 13 randomly selected colonies from the lhRNAi library showed that the size of IRs varied from 184 to 994 bp, which is appropriate for RNAi, and nine of the IRs were shown to be homologous to known genes in closely related grasses. In addition to the demonstration of the proof‐of‐concept of creating an expression‐ready library, the salt stress‐specific lhRNAi library represents a valuable resource for studying the functions of salt‐responsive genes in creeping bentgrass. The method described here is broadly applicable to all plant species where an efficient plant transformation platform is available.
Keywords	Agrostis stolonifera ; Brachypodium distachyon ; RNA interference ; outcrossing ; polyploidy ; research ; suppression subtractive hybridization ; turf grasses
Language	English
Dates of publication	2022-06
Size	p. 622-631.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ISSN	2573-1513
DOI	10.1002/its2.87
Database	NAL-Catalogue (AGRICOLA)

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Article: Interactions between autophagy and phytohormone signaling pathways in plants

Liao, Ching‐Yi / Wang, Ping / Yin, Yanhai / Bassham, Diane C.

FEBS letters. 2022 Sept., v. 596, no. 17

2022

Abstract	Autophagy is a conserved recycling process with important functions in plant growth, development, and stress responses. Phytohormones also play key roles in the regulation of some of the same processes. Increasing evidence indicates that a close relationship exists between autophagy and phytohormone signaling pathways, and the mechanisms of interaction between these pathways have begun to be revealed. Here, we review recent advances in our understanding of how autophagy regulates hormone signaling and, conversely, how hormones regulate the activity of autophagy, both in plant growth and development and in environmental stress responses. We highlight in particular recent mechanistic insights into the coordination between autophagy and signaling events controlled by the stress hormone abscisic acid and by the growth hormones brassinosteroid and cytokinin and briefly discuss potential connections between autophagy and other phytohormones.
Keywords	abscisic acid ; autophagy ; brassinosteroids ; cytokinins ; growth and development ; plant growth
Language	English
Dates of publication	2022-09
Size	p. 2198-2214.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	REVIEW
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1002/1873-3468.14355
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Article: The Association Between Lung Fluorodeoxyglucose Metabolism and Smoking History in 347 Healthy Adults.

Tong, Liang-Qian / Sui, Yan-Fang / Jiang, Sheng-Nan / Yin, Yan-Hai

Journal of asthma and allergy

2021 Volume 14, Page(s) 301–308

Abstract: Objective: This study aimed to evaluate the relationship between fluorodeoxyglucose metabolism and smoking history in healthy adults by analyzing lung standardized uptake value (SUV).: Methods: The : Results: Both the mean values of SUVmax-avr and ...

Abstract	Objective: This study aimed to evaluate the relationship between fluorodeoxyglucose metabolism and smoking history in healthy adults by analyzing lung standardized uptake value (SUV). Methods: The Results: Both the mean values of SUVmax-avr and SUVmean-avr increased based on smoking history, with non-smokers having the lowest values and current smokers the highest. Tobacco burden had a positive correlation with SUVmax-avr in current smokers ( Conclusion: The findings indicate that lung SUV increases in current heavy smokers and partially decreases after the cessation of smoking, which is in line with previous reports studied by analyzingfluorodeoxyglucose (FDG) metabolism of lung specimens.
Language	English
Publishing date	2021-03-31
Publishing country	New Zealand
Document type	Journal Article
ZDB-ID	2494877-9
ISSN	1178-6965
ISSN	1178-6965
DOI	10.2147/JAA.S302602
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